Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Recommendations for calling on and flitering ~100 low coverage samples
I have about 80-100 population-specific WGS samples with coverage around 5-10X. What modifications would you recommend in GATK best practices to suit variant calling (and VQSR) ? Also, what are the drawbacks of using the standard GVCF joint genotyping workflow for low coverage samples ?
I have one high coverage sample of about 30X; Would it help if I pool that in ?